AIMC Topic: Biological Ontologies
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Moving the mountain: analysis of the effort required to transform comparative anatomy into computable anatomy.
Database : the journal of biological databases and curation
May 13, 2015
The diverse phenotypes of living organisms have been described for centuries, and though they may be digitized, they are not readily available in a computable form. Using over 100 morphological studies, the Phenoscape project has demonstrated that by...
The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations.
Database : the journal of biological databases and curation
May 9, 2015
Biocuration has become a cornerstone for analyses in biology, and to meet needs, the amount of annotations has considerably grown in recent years. However, the reliability of these annotations varies; it has thus become necessary to be able to assess...
Toll-like receptor signaling in vertebrates: testing the integration of protein, complex, and pathway data in the protein ontology framework.
PloS one
Apr 20, 2015
The Protein Ontology (PRO) provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation o...
Generating a focused view of disease ontology cancer terms for pan-cancer data integration and analysis.
Database : the journal of biological databases and curation
Apr 4, 2015
Bio-ontologies provide terminologies for the scientific community to describe biomedical entities in a standardized manner. There are multiple initiatives that are developing biomedical terminologies for the purpose of providing better annotation, da...
Integrating ontologies of rare diseases and radiological diagnosis.
Journal of the American Medical Informatics Association : JAMIA
Mar 31, 2015
PURPOSE: The author sought to integrate an ontology of rare diseases with a large ontological model of radiological diagnosis.
MorphoCol: An ontology-based knowledgebase for the characterisation of clinically significant bacterial colony morphologies.
Journal of biomedical informatics
Mar 25, 2015
BACKGROUND: One of the major concerns of the biomedical community is the increasing prevalence of antimicrobial resistant microorganisms. Recent findings show that the diversification of colony morphology may be indicative of the expression of virule...
Assessing the impact of case sensitivity and term information gain on biomedical concept recognition.
PloS one
Mar 19, 2015
Concept recognition (CR) is a foundational task in the biomedical domain. It supports the important process of transforming unstructured resources into structured knowledge. To date, several CR approaches have been proposed, most of which focus on a ...
Comparing a knowledge-driven approach to a supervised machine learning approach in large-scale extraction of drug-side effect relationships from free-text biomedical literature.
BMC bioinformatics
Mar 18, 2015
BACKGROUND: Systems approaches to studying drug-side-effect (drug-SE) associations are emerging as an active research area for both drug target discovery and drug repositioning. However, a comprehensive drug-SE association knowledge base does not exi...
Innovative Bayesian and parsimony phylogeny of dung beetles (coleoptera, scarabaeidae, scarabaeinae) enhanced by ontology-based partitioning of morphological characters.
PloS one
Mar 17, 2015
Scarabaeine dung beetles are the dominant dung feeding group of insects and are widely used as model organisms in conservation, ecology and developmental biology. Due to the conflicts among 13 recently published phylogenies dealing with the higher-le...
Combining computational models, semantic annotations and simulation experiments in a graph database.
Database : the journal of biological databases and curation
Mar 8, 2015
Model repositories such as the BioModels Database, the CellML Model Repository or JWS Online are frequently accessed to retrieve computational models of biological systems. However, their storage concepts support only restricted types of queries and ...
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